The thing is that the free school meals are a very recent innovation (Coalition govt), and they are meant to be a long term public health intervention - to expose young children to a good variety of healthy food is meant to encourage better eating and decrease chronic health problems over a lifetime.
Just think of the current huge (and growing) burden on the NHS caused by poor lifestyle choices and poor nutrition causing diabetes, obesity, heart disease, poor dental health and many other things. The vast majority of this has been caused by a lifetime of poor nutrition and poor food choices from the 1930s onwards. Many Baby Boomers have shocking health and poor teeth from very bad childhood nutrition which has long term health effects (my mum has only about 3 teeth left after being fed pretty much on rosehip syrup, sweets and boiled potatoes for most of her first decade!)
There is a lot of recent social health science showing that, for example, middle class and higher income children have better nutrition not just because it's a family choice (and more affordable for them), but because their families can afford the food waste at a crucial time when children are starting to learn and accept a variety of different foods. Children often need to be exposed to an unfamiliar food many times before they take to accepting it and eating it. For low-income families this means that they can't afford to be buying food that their kids might not eat just to expand their food repertoire. They need to focus on food they know the kids will eat. But higher-income families are more able to absorb the cost of the food waste and continue offering (say) broccoli for ten mealtime until the child starts eating it, and so on.
This tendency to be exposed to a greater range and variety of foods and more expensive, healthier foods means that higher-income children are getting a better nutritional start in life than low-income children. It's just one of many tiny, often imperceptible ways in which social inequality and disadvantage gets perpetuated. The free school meals is one attempt to change that, since children who might not be exposed to a wide variety of different meat and veg are getting that exposure at school even if their families can't afford to do it at home.
There are also "soft" social effects too in terms of all children sitting down to eat together, as a community, so social equality and community building is another aim of the meals.
Plus it helps economically for the school meals providers to commit to providing healthy, local, fresh food as they know how many children they will be providing for over a set amount of time. The hope is that by having the free infant meals, parents will then be keen to continue paying for them at junior level. The more sustainable the finning of them is, the better and healthier the product. Who would want to go back to the school meals of the 80s or 90s, all fried pizza and chips?
I personally think the long-term benefits of the free infant meals go well beyond a small amount of food waste now - why lock kids into packed lunches and very limited eating patterns for the sake of a small amount of public money? The amount spent on these meals is minuscule compared to the big taxpayer costs of pensions, healthcare, winter fuel allowance, free bus passes, and so on. Especially when you think that a small expenditure on infant school children now could help prevent a little of the massive healthcare costs of poor nutrition sixty years down the line.
If you are concerned, OP, why not ask if the portion sizes in your school could be reduced slightly?